org.emboss.jemboss.server
Class JembossAuthServer

java.lang.Object
  org.emboss.jemboss.server.JembossAuthServer

public class JembossAuthServer

extends java.lang.Object

Jemboss Authenticated Server for Apache Axis (SOAP) web services

Field Summary

(package private) java.lang.String	embossBin emboss binary path
(package private) java.lang.String	embossData emboss data path
(package private) java.lang.String	embossPath path environment variable
private java.lang.String[]	env emboss run environment
private java.lang.String	environ emboss run environment as a string
private java.lang.String	errorLog Jemboss error log file
private java.lang.String	fs file separator
(package private) JembossParams	jp jemboss properties
private java.lang.String	logFile Jemboss log file
private java.lang.String	ls line seperator
(package private) java.lang.String	plplot plplot path
private java.lang.String	ps path separator
private java.lang.String	tmproot SOAP results directory

Constructor Summary

JembossAuthServer()

Method Summary

private void	appendToLogFile(java.lang.String logEntry, java.lang.String logFileName) Appends a log entry to the log file
java.util.Vector	call_ajax(java.lang.String fileContent, java.lang.String seqtype) Uses JNI to calculate sequence attributes using EMBOSS library call.
java.util.Vector	call_ajax(java.lang.String fileContent, java.lang.String seqtype, java.lang.String userName, byte[] passwd) Uses JNI to calculate sequence attributes using EMBOSS library call.
java.lang.Object	clone()
java.util.Vector	delete_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName, byte[] passwd) Deletes a projects saved results.
java.util.Vector	getWossname() Returns the output of the EMBOSS utility wossname
java.util.Vector	list_saved_results(java.lang.String userName, byte[] passwd) List of the saved results on the server.
private java.util.Vector	loadFilesContent(Ajax aj, java.lang.String userName, byte[] passwd, java.io.File projectDir, java.lang.String project, java.util.Vector result, java.util.Vector inFiles) Reads in files from EMBOSS output
private java.lang.String	quoteMe(java.lang.String s) Quote all tokens ready for shell scripts
private java.util.Vector	returnError(Ajax aj, java.lang.String msg) Report the stderr and stdout to error logs
java.util.Vector	run_prog(java.lang.String embossCommand, java.lang.String options, java.util.Vector inFiles, java.lang.String userName, byte[] passwd) Run an emboss application
private void	runAsBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand) Submit to a batch queue
private void	runAsGNQSBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand) Submit to a Generic NQS batch queue.
private void	runAsPBSBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand) Submit to a OpenPBS batch queue.
java.util.Vector	save_project_file(java.lang.String project, java.lang.String filename, java.lang.String notes, java.lang.String userName, byte[] passwd) Save a file to a project directory on the server.
java.util.Vector	show_acd(java.lang.String appName) Retrieves the ACD file of an application.
java.util.Vector	show_db() Returns the databases held on the server
java.util.Vector	show_help(java.lang.String applName) Returns the help for an application as given by 'tfm'
java.util.Vector	show_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName, byte[] passwd) Returns the results for a saved project.
java.util.Vector	update_result_status(java.lang.String prog, java.lang.String opt, java.util.Vector resToQuery, java.lang.String userName, byte[] passwd) Used to provide information on the batch/background processes.
private boolean	verifyUser(Ajax aj, java.lang.String userName, byte[] passwd, java.util.Vector res) Verify the username/passwd

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

tmproot

private java.lang.String tmproot

SOAP results directory

logFile

private java.lang.String logFile

Jemboss log file

errorLog

private java.lang.String errorLog

Jemboss error log file

fs

private java.lang.String fs

file separator

ps

private java.lang.String ps

path separator

ls

private java.lang.String ls

line seperator

jp

JembossParams jp

jemboss properties

plplot

java.lang.String plplot

plplot path

embossData

java.lang.String embossData

emboss data path

embossBin

java.lang.String embossBin

emboss binary path

embossPath

java.lang.String embossPath

path environment variable

env

private java.lang.String[] env

emboss run environment

environ

private java.lang.String environ

emboss run environment as a string

Constructor Detail

JembossAuthServer

public JembossAuthServer()

Method Detail

show_acd

public java.util.Vector show_acd(java.lang.String appName)

Retrieves the ACD file of an application.

Parameters:

appName - application name

Returns:

Vector of containing the ACD string

getWossname

public java.util.Vector getWossname()

Returns the output of the EMBOSS utility wossname

Returns:

wossname output

show_help

public java.util.Vector show_help(java.lang.String applName)

Returns the help for an application as given by 'tfm'

Parameters:

applName - application name

Returns:

help

call_ajax

public java.util.Vector call_ajax(java.lang.String fileContent,
                                  java.lang.String seqtype,
                                  java.lang.String userName,
                                  byte[] passwd)

Uses JNI to calculate sequence attributes using EMBOSS library call.

Parameters:

fileContent - sequence filename or database entry

seqtype - sequence type (seqset/sequence)

userName - username

passwd - passwd

Returns:

sequence length, weight & type (protein/nucleotide)

call_ajax

public java.util.Vector call_ajax(java.lang.String fileContent,
                                  java.lang.String seqtype)

Uses JNI to calculate sequence attributes using EMBOSS library call.

Parameters:

fileContent - sequence filename or database entry

seqtype - sequence type (seqset/sequence)

Returns:

sequence length, weight & type (protein/nucleotide)

show_db

public java.util.Vector show_db()

Returns the databases held on the server

Returns:

output from 'showdb'

run_prog

public java.util.Vector run_prog(java.lang.String embossCommand,
                                 java.lang.String options,
                                 java.util.Vector inFiles,
                                 java.lang.String userName,
                                 byte[] passwd)

Run an emboss application

Parameters:

embossCommand - command line to run

options - options

inFiles - input files

userName - userName

passwd - passwd

Returns:

output files from application run

quoteMe

private java.lang.String quoteMe(java.lang.String s)

Quote all tokens ready for shell scripts

Parameters:

s - text to quote

Returns:

quoted text

runAsPBSBatch

private void runAsPBSBatch(Ajax aj,
                           java.lang.String userName,
                           byte[] passwd,
                           java.lang.String project,
                           java.lang.String embossCommand)

Submit to a OpenPBS batch queue. This method creates a script for submission to a batch queueing system.

Parameters:

aj - ajax/jni

userName - username

passwd - passwd

project - project directory

embossCommand - emboss command

runAsGNQSBatch

private void runAsGNQSBatch(Ajax aj,
                            java.lang.String userName,
                            byte[] passwd,
                            java.lang.String project,
                            java.lang.String embossCommand)

Submit to a Generic NQS batch queue. This method creates a script for submission to a batch queueing system.

Parameters:

aj - ajax/jni

userName - username

passwd - passwd

project - project directory

embossCommand - emboss command

runAsBatch

private void runAsBatch(Ajax aj,
                        java.lang.String userName,
                        byte[] passwd,
                        java.lang.String project,
                        java.lang.String embossCommand)

Submit to a batch queue

Parameters:

aj - ajax/jni

userName - username

passwd - passwd

project - project directory

embossCommand - emboss command

show_saved_results

public java.util.Vector show_saved_results(java.lang.String project,
                                           java.lang.String cl,
                                           java.lang.String userName,
                                           byte[] passwd)

Returns the results for a saved project.

Parameters:

project - project directory name

cl - unused if showing all results otherwise this is the name of the file to display

userName - username

passwd - passwd

Returns:

saved results files

save_project_file

public java.util.Vector save_project_file(java.lang.String project,
                                          java.lang.String filename,
                                          java.lang.String notes,
                                          java.lang.String userName,
                                          byte[] passwd)

Save a file to a project directory on the server.

Returns:

message

delete_saved_results

public java.util.Vector delete_saved_results(java.lang.String project,
                                             java.lang.String cl,
                                             java.lang.String userName,
                                             byte[] passwd)

Deletes a projects saved results.

Parameters:

project - project directory name

cl - unused

userName - username

passwd - passwd

Returns:

message

list_saved_results

public java.util.Vector list_saved_results(java.lang.String userName,
                                           byte[] passwd)

List of the saved results on the server.

Parameters:

userName - username

passwd - passwd

Returns:

list of the saved results.

appendToLogFile

private void appendToLogFile(java.lang.String logEntry,
                             java.lang.String logFileName)

Appends a log entry to the log file

Parameters:

logEntry - entry to add to log file

logFileName - log file name

loadFilesContent

private java.util.Vector loadFilesContent(Ajax aj,
                                          java.lang.String userName,
                                          byte[] passwd,
                                          java.io.File projectDir,
                                          java.lang.String project,
                                          java.util.Vector result,
                                          java.util.Vector inFiles)

Reads in files from EMBOSS output

Parameters:

aj - ajax/jni

userName - username

passwd - passwd

projectDir - project directory

project - project name

result - results

inFiles - input files

Returns:

result

update_result_status

public java.util.Vector update_result_status(java.lang.String prog,
                                             java.lang.String opt,
                                             java.util.Vector resToQuery,
                                             java.lang.String userName,
                                             byte[] passwd)

Used to provide information on the batch/background processes.

Parameters:

prog - program

opt - options

resToQuery - results to query

userName - username

passwd - passwd

verifyUser

private boolean verifyUser(Ajax aj,
                           java.lang.String userName,
                           byte[] passwd,
                           java.util.Vector res)

Verify the username/passwd

Parameters:

aj - ajax/jni

userName - username

passwd - password

res - results vector

Returns:

true if authenticated ok

returnError

private java.util.Vector returnError(Ajax aj,
                                     java.lang.String msg)

Report the stderr and stdout to error logs

Parameters:

aj - ajax/jni

msg - message

Returns:

vector containing the message

clone

public final java.lang.Object clone()
                             throws java.lang.CloneNotSupportedException

Throws:

java.lang.CloneNotSupportedException